The original Clandestine was a pipe-and-drum quartet in Houston. Original member bagpiper E.J. Jones moved to Pittsburgh, met guitarist and singer Jen Hamel in Pittsburgh, and convinced her to return to Houston to perform as part of Clandestine. In 1995, fiddle player Gregory McQueen joined. The first disc (The Ale is Dear) featured this trio. In 1996 percussionist and singer Emily Dugas joined, and the remaining 3 discs include all 4 members. Jen Hamel and Emily Dugas both sang. In February 2003 the band performed their last show in that original incarnation.

In 2005, E.J., Emily and Gregory began playing with various other artists as the Emily Dugas Band. In 2006, with Jen's blessing, they officially reformed Clandestine with themselves and a fourth member, Al Cofrin, on Irish cittern, folk guitar, and medieval bagpipes. The band made their formal debut as Clandestine at the Mucky Duck Pub in Houston on St. Andrew's Day, November 30, 2006.